pcalc: Perform purity calculation on a peak matrix

In msPurity: Automated Evaluation of Precursor Ion Purity for Mass Spectrometry Based Fragmentation in Metabolomics

Description

This is the main purity calculation that is performed in purityX, purityD and purityA.

• Takes in a matrix of peaks

• gets isolation window based on mzmin mzmax

• locates the mz target in the peak matrix

• removes isotopic peaks

• removes any peaks below limit (percentage of target peak intensity)

• normalises

• Calculates purity: Divides the target peak intensity by the total peak intensity for the isolation window

Usage

pcalc(
  peaks,
  mzmin,
  mzmax,
  mztarget,
  ppm = NA,
  iwNorm = FALSE,
  iwNormFun = NULL,
  ilim = 0,
  targetMinMZ = NA,
  targetMaxMZ = NA,
  isotopes = FALSE,
  im = NULL
)

Arguments

peaks	matrix; Matrix of peaks consisting of 2 columns: mz and i
mzmin	numeric; Isolation window (min)
mzmax	numeric; Isolation window (max)
mztarget	numeric; The mz window to target in the isolation window
ppm	numeric; PPM tolerance for the target mz value. If NA will presume targetMinMZ and targetMaxMZ will be used
iwNorm	boolean; If TRUE then the intensity of the isolation window will be normalised based on the iwNormFun function
iwNormFun	function; A function to normalise the isolation window intensity. The default function is very generalised and just accounts for edge effects
ilim	numeric; All peaks less than this percentage of the target peak will be removed from the purity calculation, default is 5% (0.05)
targetMinMZ	numeric; Range to look for the mztarget (min)
targetMaxMZ	numeric; Range to look for the mztarget (max)
isotopes	boolean; TRUE if isotopes are to be removed
im	matrix; Isotope matrix, default removes C13 isotopes (single, double and triple bonds)

Value

a vector of the purity score and the number of peaks in the window e.g c(purity, pknm)

Examples

pm <- rbind(c(100, 1000),c(101.003, 10))
pcalc(pm, mzmin = 98, mzmax = 102, mztarget=100, ppm=5)
pcalc(pm, mzmin = 98, mzmax = 102, mztarget=100, ppm=5, isotopes = TRUE)

msPurity documentation built on Jan. 14, 2021, 2:44 a.m.